Those applications are Google's sole bargaining point with handset manufacturers and carriers to have them build Android devices meeting certain requirements in order to make sure the Google Experience is up to par. If carrier/manufacturers don't agree to Google's terms, then they aren't allowed to distribute those "killer" apps with their phones. Making those apps still available to end-users who potentially may or may not have a Google Experience-worthy phone would kill much of their bargaining factor...
That said, as a user of CyanogenMod on my G1, I'd be absolutely heartbroken if his builds could no longer distribute these apps.